Nemo and his fellow prisoners at the penal colony in Kalpani are forced to build a giant submarine - the Nautilus. As soon as it is ready, Nemo and his confidants plan to escape using the submarine. But when Director Crawley of the ruthless East India Trading Company arrives and demands that the Nautilus be immediately moved to Bombay to be outfitted, Nemo is forced to advance his plans, with whomever he can gather for a crew.

When some of the crew try to leave the Nautilus and swim to shore, they are discovered by the company's emissaries and forced back. Now the Nautilus must go out to sea to avoid capture. An unexpected encounter with a whaler slows them down and just as they are almost there they are forced below the surface for a game of cat and mouse.

Captain Nemo and his crew are forced to make a stop on the island of Karajan for water and supplies. Nemo discovers a shocking truth and Humility and the crew find out who Nemo really is.

Captain Nemo and his starving crew go ashore on a seemingly deserted island in search of food. When Blaster goes missing, Nemo and Humility embark on a daring rescue mission but soon encounter a giant electric eel.

When an eerie red glow appears, the giant eel suddenly releases the Nautilus, it turns out to be a chain of underwater volcanoes. Without steering power, the Nautilus continues to sink towards the dangerous lava - and it soon becomes clear that only Humility can save the crew.

The underwater volcanoes turn out to reveal a clue to the legendary underwater city of Atlantis. A small group goes exploring and finds what appears to be an ancient outpost of the lost civilization, but also realizes that it is home to terrifying sea lilies and the crew must fight for their lives.

A daring battle between the Company ships Dreadnought and Nautilus leaves both stranded in the Arctic ice, leading to an uneasy truce. Nemo reunites with a friend from his past and is shaken by more revelations about his father.

When it is revealed that Nemo has been too daring and put the crew in danger, they lock him in his cabin and Boniface takes command instead. At the magnetic north pole, the problems pile up. Nemo must unite his divided crew by telling them who he really is.

When Nautilus finally arrives at the treasure, they realize that it has not been forgotten at all, on the contrary, it is guarded by wild warriors. Nemo feels that he has led his crew to the end of the world - for nothing.